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<li class="navelem"><a class="el" href="dir_3dc1dabd28ba78e072d14d3fcfc90454.html">SPHINXsys</a></li><li class="navelem"><a class="el" href="dir_48ea983704c43b6d88c1fa3f4d09e369.html">src</a></li><li class="navelem"><a class="el" href="dir_0a0d9ef1793521534f0094f317758287.html">shared</a></li><li class="navelem"><a class="el" href="dir_536e372c8df10cac250269553cb892e1.html">materials</a></li>  </ul>
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<div class="title">diffusion_reaction.h</div>  </div>
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<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">/* -------------------------------------------------------------------------*</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">*                               SPHinXsys                                   *</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">* --------------------------------------------------------------------------*</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">* SPHinXsys (pronunciation: s&#39;finksis) is an acronym from Smoothed Particle *</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">* Hydrodynamics for industrial compleX systems. It provides C++ APIs for    *</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">* physical accurate simulation and aims to model coupled industrial dynamic *</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">* systems including fluid, solid, multi-body dynamics and beyond with SPH   *</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">* (smoothed particle hydrodynamics), a meshless computational method using  *</span></div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">* particle discretization.                                                  *</span></div>
<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;<span class="comment">*                                                                           *</span></div>
<div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="comment">* SPHinXsys is partially funded by German Research Foundation               *</span></div>
<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;<span class="comment">* (Deutsche Forschungsgemeinschaft) DFG HU1527/6-1, HU1527/10-1             *</span></div>
<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="comment">* and HU1527/12-1.                                                          *</span></div>
<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="comment">*                                                                           *</span></div>
<div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;<span class="comment">* Portions copyright (c) 2017-2020 Technical University of Munich and       *</span></div>
<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<span class="comment">* the authors&#39; affiliations.                                                *</span></div>
<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="comment">*                                                                           *</span></div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="comment">* Licensed under the Apache License, Version 2.0 (the &quot;License&quot;); you may   *</span></div>
<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="comment">* not use this file except in compliance with the License. You may obtain a *</span></div>
<div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;<span class="comment">* copy of the License at http://www.apache.org/licenses/LICENSE-2.0.        *</span></div>
<div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;<span class="comment">*                                                                           *</span></div>
<div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<span class="comment">* --------------------------------------------------------------------------*/</span></div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="preprocessor">#pragma once</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160; </div>
<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="base__material_8h.html">base_material.h</a>&quot;</span></div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="solid__particles_8h.html">solid_particles.h</a>&quot;</span></div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160; </div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="preprocessor">#include &lt;map&gt;</span></div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="preprocessor">#include &lt;functional&gt;</span></div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="keyword">using namespace </span>std::placeholders;</div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160; </div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="keyword">namespace </span><a class="code" href="namespace_s_p_h.html">SPH</a> </div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;{</div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div>
<div class="line"><a name="l00043"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_particles.html">   43</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html">DiffusionReactionParticles</a>;</div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_electro_physiology_particles.html">ElectroPhysiologyParticles</a>;</div>
<div class="line"><a name="l00049"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_base_diffusion.html">   49</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_base_diffusion.html">BaseDiffusion</a> : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_base_material.html">BaseMaterial</a></div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;    {</div>
<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;    <span class="keyword">public</span>:</div>
<div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;        <a class="code" href="class_s_p_h_1_1_base_diffusion.html">BaseDiffusion</a>(<span class="keywordtype">size_t</span> diffusion_species_index, <span class="keywordtype">size_t</span> gradient_species_index) : </div>
<div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;            <a class="code" href="class_s_p_h_1_1_base_material.html">BaseMaterial</a>(), diffusion_species_index_(diffusion_species_index), </div>
<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;            gradient_species_index_(gradient_species_index) {};</div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_base_diffusion.html">BaseDiffusion</a>() {};</div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160; </div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;        <span class="keywordtype">size_t</span> diffusion_species_index_;</div>
<div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;        <span class="keywordtype">size_t</span> gradient_species_index_;</div>
<div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160; </div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;        <span class="keyword">virtual</span> Real getReferenceDiffusivity() = 0;</div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;        <span class="keyword">virtual</span> Real getInterParticleDiffusionCoff(<span class="keywordtype">size_t</span> particle_i, <span class="keywordtype">size_t</span> particle_j, Vecd&amp; direction_from_j_to_i) = 0;</div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;    };</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160; </div>
<div class="line"><a name="l00068"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_isotropic_diffusion.html">   68</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_isotropic_diffusion.html">IsotropicDiffusion</a> : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_base_diffusion.html">BaseDiffusion</a></div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;    {</div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;    <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00071"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_isotropic_diffusion.html#ab1406312fbceea5607a7edd01453920f">   71</a></span>&#160;        Real <a class="code" href="class_s_p_h_1_1_isotropic_diffusion.html#ab1406312fbceea5607a7edd01453920f">diff_cf_</a>; </div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;    <span class="keyword">public</span>:</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;        <a class="code" href="class_s_p_h_1_1_isotropic_diffusion.html">IsotropicDiffusion</a>(<span class="keywordtype">size_t</span> diffusion_species_index, <span class="keywordtype">size_t</span> gradient_species_index,</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;            Real diff_cf = 1.0) : <a class="code" href="class_s_p_h_1_1_base_diffusion.html">BaseDiffusion</a>(diffusion_species_index, gradient_species_index),</div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;            diff_cf_(diff_cf) {};</div>
<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_isotropic_diffusion.html">IsotropicDiffusion</a>() {};</div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160; </div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;        <span class="keyword">virtual</span> <a class="code" href="class_real.html">Real</a> getReferenceDiffusivity()<span class="keyword"> override </span>{ <span class="keywordflow">return</span> diff_cf_; };</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;        <span class="keyword">virtual</span> <a class="code" href="class_real.html">Real</a> getInterParticleDiffusionCoff(<span class="keywordtype">size_t</span> particle_i, <span class="keywordtype">size_t</span> particle_j, <a class="code" href="class_vecd.html">Vecd</a>&amp; direction_from_j_to_i)<span class="keyword"> override</span></div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;<span class="keyword">        </span>{</div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;            <span class="keywordflow">return</span> diff_cf_;</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;        };</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;    };</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160; </div>
<div class="line"><a name="l00090"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_directional_diffusion.html">   90</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_directional_diffusion.html">DirectionalDiffusion</a> : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_isotropic_diffusion.html">IsotropicDiffusion</a></div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;    {</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;    <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00093"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_directional_diffusion.html#a6c1e25784f768cb1caffb38ab17332e4">   93</a></span>&#160;        Vecd <a class="code" href="class_s_p_h_1_1_directional_diffusion.html#a6c1e25784f768cb1caffb38ab17332e4">bias_direction_</a>;   </div>
<div class="line"><a name="l00094"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_directional_diffusion.html#a2d7e6efe0bd23b2f8a483563270298c5">   94</a></span>&#160;        Real <a class="code" href="class_s_p_h_1_1_directional_diffusion.html#a2d7e6efe0bd23b2f8a483563270298c5">bias_diff_cf_</a>;     </div>
<div class="line"><a name="l00095"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_directional_diffusion.html#abc4879e198a2fd6cf4bb19c68e8a3d4d">   95</a></span>&#160;        Matd <a class="code" href="class_s_p_h_1_1_directional_diffusion.html#abc4879e198a2fd6cf4bb19c68e8a3d4d">transformed_diffusivity_</a>;  </div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;        <span class="keywordtype">void</span> initializeDirectionalDiffusivity(Real diff_cf, Real bias_diff_cf, Vecd bias_direction);</div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;    <span class="keyword">public</span>:</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;        <a class="code" href="class_s_p_h_1_1_directional_diffusion.html">DirectionalDiffusion</a>(<span class="keywordtype">size_t</span> diffusion_species_index, <span class="keywordtype">size_t</span> gradient_species_index,</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;            Real diff_cf, Real bias_diff_cf, Vecd bias_direction) : </div>
<div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;            <a class="code" href="class_s_p_h_1_1_isotropic_diffusion.html">IsotropicDiffusion</a>(diffusion_species_index, gradient_species_index, diff_cf), </div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;            bias_direction_(bias_direction), bias_diff_cf_(bias_diff_cf), </div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;            transformed_diffusivity_(1.0) </div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;        {</div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;            initializeDirectionalDiffusivity(diff_cf, bias_diff_cf, bias_direction);</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;        };</div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_directional_diffusion.html">DirectionalDiffusion</a>() {};</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160; </div>
<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;        <span class="keyword">virtual</span> <a class="code" href="class_real.html">Real</a> getReferenceDiffusivity()<span class="keyword"> override</span></div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;<span class="keyword">        </span>{</div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;            <span class="keywordflow">return</span> SMAX(diff_cf_, diff_cf_ + bias_diff_cf_);</div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;        };</div>
<div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160; </div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;        <span class="keyword">virtual</span> <a class="code" href="class_real.html">Real</a> getInterParticleDiffusionCoff(<span class="keywordtype">size_t</span> particle_index_i, </div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;            <span class="keywordtype">size_t</span> particle_index_j, <a class="code" href="class_vecd.html">Vecd</a>&amp; inter_particle_direction)<span class="keyword"> override</span></div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;<span class="keyword">        </span>{</div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;            <a class="code" href="class_vecd.html">Vecd</a> grad_ij = transformed_diffusivity_ * inter_particle_direction;</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;            <span class="keywordflow">return</span> 1.0 / grad_ij.scalarNormSqr();</div>
<div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;        };</div>
<div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;    };</div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160; </div>
<div class="line"><a name="l00126"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_local_directional_diffusion.html">  126</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_local_directional_diffusion.html">LocalDirectionalDiffusion</a> : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_directional_diffusion.html">DirectionalDiffusion</a></div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;    {</div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;    <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;        StdLargeVec&lt;Vecd&gt; local_bias_direction_;</div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;        StdLargeVec&lt;Matd&gt; local_transformed_diffusivity_;</div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160; </div>
<div class="line"><a name="l00132"></a><span class="lineno">  132</span>&#160;        <span class="keywordtype">void</span> initializeFiberDirection();</div>
<div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;    <span class="keyword">public</span>:</div>
<div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;        <a class="code" href="class_s_p_h_1_1_local_directional_diffusion.html">LocalDirectionalDiffusion</a>(<span class="keywordtype">size_t</span> diffusion_species_index, <span class="keywordtype">size_t</span> gradient_species_index,</div>
<div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;            Real diff_cf, Real bias_diff_cf, Vecd bias_direction)</div>
<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;            : <a class="code" href="class_s_p_h_1_1_directional_diffusion.html">DirectionalDiffusion</a>(diffusion_species_index, gradient_species_index, diff_cf, bias_diff_cf, bias_direction) {};</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_local_directional_diffusion.html">LocalDirectionalDiffusion</a>() {};</div>
<div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;        <span class="keyword">virtual</span> Real getInterParticleDiffusionCoff(<span class="keywordtype">size_t</span> particle_index_i, <span class="keywordtype">size_t</span> particle_index_j, Vecd&amp; inter_particle_direction)<span class="keyword"> override</span></div>
<div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;<span class="keyword">        </span>{</div>
<div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;            Matd trans_diffusivity = getAverageValue(local_transformed_diffusivity_[particle_index_i], local_transformed_diffusivity_[particle_index_j]);</div>
<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;            Vecd grad_ij = trans_diffusivity * inter_particle_direction;</div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;            <span class="keywordflow">return</span> 1.0 / grad_ij.scalarNormSqr();</div>
<div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;        };</div>
<div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> assignBaseParticles(<a class="code" href="class_s_p_h_1_1_base_particles.html">BaseParticles</a>* base_particles);</div>
<div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> readFromXmlForLocalParameters(std::string&amp; filefullpath) <span class="keyword">override</span>;</div>
<div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;    };</div>
<div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160; </div>
<div class="line"><a name="l00149"></a><span class="lineno"><a class="line" href="namespace_s_p_h.html#a341a68e44d4d73463e7fcfe4f09e521e">  149</a></span>&#160;    <span class="keyword">typedef</span> std::function&lt;Real(StdVec&lt;StdLargeVec&lt;Real&gt;&gt;&amp;, <span class="keywordtype">size_t</span> particle_i)&gt; <a class="code" href="namespace_s_p_h.html#a341a68e44d4d73463e7fcfe4f09e521e">ReactionFunctor</a>;</div>
<div class="line"><a name="l00154"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_base_reaction_model.html">  154</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_base_reaction_model.html">BaseReactionModel</a></div>
<div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;    {</div>
<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;    <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> assignDerivedReactionParameters() = 0;</div>
<div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;    <span class="keyword">public</span>:</div>
<div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;        <a class="code" href="class_s_p_h_1_1_base_reaction_model.html">BaseReactionModel</a>() {};</div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_base_reaction_model.html">BaseReactionModel</a>() {};</div>
<div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160; </div>
<div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;        <a class="code" href="namespace_s_p_h.html#abae56fd7f25f13487c7943ce4681d0ce">IndexVector</a> reactive_species_;</div>
<div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;        StdVec&lt;ReactionFunctor&gt; get_production_rates_;</div>
<div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;        StdVec&lt;ReactionFunctor&gt; get_loss_rates_;</div>
<div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;    };</div>
<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160; </div>
<div class="line"><a name="l00173"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_electro_physiology_reaction.html">  173</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_electro_physiology_reaction.html">ElectroPhysiologyReaction</a> : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_base_reaction_model.html">BaseReactionModel</a></div>
<div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;    {</div>
<div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;    <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00176"></a><span class="lineno">  176</span>&#160;        Real k_a_;</div>
<div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;        <span class="keywordtype">size_t</span> voltage_;</div>
<div class="line"><a name="l00178"></a><span class="lineno">  178</span>&#160;        <span class="keywordtype">size_t</span> gate_variable_;</div>
<div class="line"><a name="l00179"></a><span class="lineno">  179</span>&#160;        <span class="keywordtype">size_t</span> active_contraction_stress_;</div>
<div class="line"><a name="l00180"></a><span class="lineno">  180</span>&#160; </div>
<div class="line"><a name="l00181"></a><span class="lineno">  181</span>&#160;        <span class="keyword">virtual</span> Real getProductionRateIonicCurrent(StdVec&lt;StdLargeVec&lt;Real&gt;&gt;&amp; species, <span class="keywordtype">size_t</span> particle_i) = 0;</div>
<div class="line"><a name="l00182"></a><span class="lineno">  182</span>&#160;        <span class="keyword">virtual</span> Real getLossRateIonicCurrent(StdVec&lt;StdLargeVec&lt;Real&gt;&gt;&amp; species, <span class="keywordtype">size_t</span> particle_i) = 0;</div>
<div class="line"><a name="l00183"></a><span class="lineno">  183</span>&#160;        <span class="keyword">virtual</span> Real getProductionRateGateVariable(StdVec&lt;StdLargeVec&lt;Real&gt;&gt;&amp; species, <span class="keywordtype">size_t</span> particle_i) = 0;</div>
<div class="line"><a name="l00184"></a><span class="lineno">  184</span>&#160;        <span class="keyword">virtual</span> Real getLossRateGateVariable(StdVec&lt;StdLargeVec&lt;Real&gt;&gt;&amp; species, <span class="keywordtype">size_t</span> particle_i) = 0;</div>
<div class="line"><a name="l00185"></a><span class="lineno">  185</span>&#160;        <span class="keyword">virtual</span> Real getProductionActiveContractionStress(StdVec&lt;StdLargeVec&lt;Real&gt;&gt;&amp; species, <span class="keywordtype">size_t</span> particle_i);</div>
<div class="line"><a name="l00186"></a><span class="lineno">  186</span>&#160;        <span class="keyword">virtual</span> Real getLossRateActiveContractionStress(StdVec&lt;StdLargeVec&lt;Real&gt;&gt;&amp; species, <span class="keywordtype">size_t</span> particle_i);</div>
<div class="line"><a name="l00187"></a><span class="lineno">  187</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> assignDerivedReactionParameters()<span class="keyword"> override </span>{};</div>
<div class="line"><a name="l00188"></a><span class="lineno">  188</span>&#160;    <span class="keyword">public</span>:</div>
<div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;        <a class="code" href="class_s_p_h_1_1_electro_physiology_reaction.html">ElectroPhysiologyReaction</a>() : <a class="code" href="class_s_p_h_1_1_base_reaction_model.html">BaseReactionModel</a>(), k_a_(1.0),</div>
<div class="line"><a name="l00190"></a><span class="lineno">  190</span>&#160;            voltage_(0), gate_variable_(1), active_contraction_stress_(2) {};</div>
<div class="line"><a name="l00191"></a><span class="lineno">  191</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_electro_physiology_reaction.html">ElectroPhysiologyReaction</a>() {};</div>
<div class="line"><a name="l00192"></a><span class="lineno">  192</span>&#160;        <span class="keywordtype">void</span> initializeElectroPhysiologyReaction(<span class="keywordtype">size_t</span> voltage,</div>
<div class="line"><a name="l00193"></a><span class="lineno">  193</span>&#160;            <span class="keywordtype">size_t</span> gate_variable, <span class="keywordtype">size_t</span> active_contraction_stress);</div>
<div class="line"><a name="l00194"></a><span class="lineno">  194</span>&#160;    };</div>
<div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160; </div>
<div class="line"><a name="l00196"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_aliev_panfilow_model.html">  196</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_aliev_panfilow_model.html">AlievPanfilowModel</a> : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_electro_physiology_reaction.html">ElectroPhysiologyReaction</a></div>
<div class="line"><a name="l00197"></a><span class="lineno">  197</span>&#160;    {</div>
<div class="line"><a name="l00198"></a><span class="lineno">  198</span>&#160;    <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00200"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_aliev_panfilow_model.html#ac926a3fcc24e3f7b65e2d87fa59662b4">  200</a></span>&#160;        Real <a class="code" href="class_s_p_h_1_1_aliev_panfilow_model.html#ac926a3fcc24e3f7b65e2d87fa59662b4">k_</a>, a_, b_, mu_1_, mu_2_, epsilon_, c_m_;</div>
<div class="line"><a name="l00201"></a><span class="lineno">  201</span>&#160; </div>
<div class="line"><a name="l00202"></a><span class="lineno">  202</span>&#160;        <span class="keyword">virtual</span> Real getProductionRateIonicCurrent(StdVec&lt;StdLargeVec&lt;Real&gt;&gt;&amp; species, <span class="keywordtype">size_t</span> particle_i) <span class="keyword">override</span>;</div>
<div class="line"><a name="l00203"></a><span class="lineno">  203</span>&#160;        <span class="keyword">virtual</span> Real getLossRateIonicCurrent(StdVec&lt;StdLargeVec&lt;Real&gt;&gt;&amp; species, <span class="keywordtype">size_t</span> particle_i) <span class="keyword">override</span>;</div>
<div class="line"><a name="l00204"></a><span class="lineno">  204</span>&#160;        <span class="keyword">virtual</span> Real getProductionRateGateVariable(StdVec&lt;StdLargeVec&lt;Real&gt;&gt;&amp; species, <span class="keywordtype">size_t</span> particle_i) <span class="keyword">override</span>;</div>
<div class="line"><a name="l00205"></a><span class="lineno">  205</span>&#160;        <span class="keyword">virtual</span> Real getLossRateGateVariable(StdVec&lt;StdLargeVec&lt;Real&gt;&gt;&amp; species, <span class="keywordtype">size_t</span> particle_i) <span class="keyword">override</span>;</div>
<div class="line"><a name="l00206"></a><span class="lineno">  206</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> assignDerivedReactionParameters()<span class="keyword"> override </span></div>
<div class="line"><a name="l00207"></a><span class="lineno">  207</span>&#160;<span class="keyword">        </span>{</div>
<div class="line"><a name="l00208"></a><span class="lineno">  208</span>&#160;            ElectroPhysiologyReaction::assignDerivedReactionParameters();</div>
<div class="line"><a name="l00209"></a><span class="lineno">  209</span>&#160;        };</div>
<div class="line"><a name="l00210"></a><span class="lineno">  210</span>&#160;    <span class="keyword">public</span>:</div>
<div class="line"><a name="l00211"></a><span class="lineno">  211</span>&#160;        <a class="code" href="class_s_p_h_1_1_aliev_panfilow_model.html">AlievPanfilowModel</a>() : <a class="code" href="class_s_p_h_1_1_electro_physiology_reaction.html">ElectroPhysiologyReaction</a>(),</div>
<div class="line"><a name="l00212"></a><span class="lineno">  212</span>&#160;            k_(0.0), a_(0.0), b_(0.0), mu_1_(0.0), mu_2_(0.0),</div>
<div class="line"><a name="l00213"></a><span class="lineno">  213</span>&#160;            epsilon_(0.0), c_m_(0.0) {};</div>
<div class="line"><a name="l00214"></a><span class="lineno">  214</span>&#160;        <span class="keyword">virtual</span> ~AlievPanfilowModel() {};</div>
<div class="line"><a name="l00215"></a><span class="lineno">  215</span>&#160;    };</div>
<div class="line"><a name="l00216"></a><span class="lineno">  216</span>&#160;    </div>
<div class="line"><a name="l00221"></a><span class="lineno">  221</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class</span> BaseParticlesType = BaseParticles, <span class="keyword">class</span> BaseMaterialType = BaseMaterial&gt;</div>
<div class="line"><a name="l00222"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_material.html">  222</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html">DiffusionReactionMaterial</a> : <span class="keyword">public</span> BaseMaterialType</div>
<div class="line"><a name="l00223"></a><span class="lineno">  223</span>&#160;    {</div>
<div class="line"><a name="l00224"></a><span class="lineno">  224</span>&#160;    <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00225"></a><span class="lineno">  225</span>&#160; </div>
<div class="line"><a name="l00226"></a><span class="lineno">  226</span>&#160;        <span class="keywordtype">size_t</span> number_of_species_;</div>
<div class="line"><a name="l00227"></a><span class="lineno">  227</span>&#160;        <span class="keywordtype">size_t</span> number_of_diffusion_species_;</div>
<div class="line"><a name="l00228"></a><span class="lineno">  228</span>&#160;        std::map&lt;std::string, size_t&gt; species_indexes_map_;</div>
<div class="line"><a name="l00229"></a><span class="lineno">  229</span>&#160;        StdVec&lt;BaseDiffusion*&gt; species_diffusion_;</div>
<div class="line"><a name="l00230"></a><span class="lineno">  230</span>&#160;        <a class="code" href="class_s_p_h_1_1_base_reaction_model.html">BaseReactionModel</a>* species_reaction_;</div>
<div class="line"><a name="l00231"></a><span class="lineno">  231</span>&#160;        <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html">DiffusionReactionParticles&lt;BaseParticlesType, BaseMaterialType&gt;</a>* diffusion_reaction_particles_;</div>
<div class="line"><a name="l00232"></a><span class="lineno">  232</span>&#160; </div>
<div class="line"><a name="l00233"></a><span class="lineno">  233</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> assignDerivedMaterialParameters()<span class="keyword"> override </span></div>
<div class="line"><a name="l00234"></a><span class="lineno">  234</span>&#160;<span class="keyword">        </span>{</div>
<div class="line"><a name="l00235"></a><span class="lineno">  235</span>&#160;            BaseMaterialType::assignDerivedMaterialParameters();</div>
<div class="line"><a name="l00236"></a><span class="lineno">  236</span>&#160;        };</div>
<div class="line"><a name="l00237"></a><span class="lineno">  237</span>&#160; </div>
<div class="line"><a name="l00238"></a><span class="lineno">  238</span>&#160;        <span class="keywordtype">void</span> insertASpecies(std::string species_name)</div>
<div class="line"><a name="l00239"></a><span class="lineno">  239</span>&#160;        {</div>
<div class="line"><a name="l00240"></a><span class="lineno">  240</span>&#160;            species_indexes_map_.insert(make_pair(species_name, number_of_species_));</div>
<div class="line"><a name="l00241"></a><span class="lineno">  241</span>&#160;            number_of_species_++;</div>
<div class="line"><a name="l00242"></a><span class="lineno">  242</span>&#160;        };</div>
<div class="line"><a name="l00243"></a><span class="lineno">  243</span>&#160;    <span class="keyword">public</span>:</div>
<div class="line"><a name="l00245"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_material.html#ac3b04fe5b64e8374b18142c63dcadc74">  245</a></span>&#160;        <a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html#ac3b04fe5b64e8374b18142c63dcadc74">DiffusionReactionMaterial</a>() </div>
<div class="line"><a name="l00246"></a><span class="lineno">  246</span>&#160;            : BaseMaterialType(), number_of_species_(0), species_reaction_(NULL) </div>
<div class="line"><a name="l00247"></a><span class="lineno">  247</span>&#160;        {</div>
<div class="line"><a name="l00248"></a><span class="lineno">  248</span>&#160;            BaseMaterialType::material_name_ = <span class="stringliteral">&quot;DiffusionMaterial&quot;</span>;</div>
<div class="line"><a name="l00249"></a><span class="lineno">  249</span>&#160;        };</div>
<div class="line"><a name="l00251"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_material.html#a129c308dd850749a9e8a5161630121f9">  251</a></span>&#160;        <a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html#a129c308dd850749a9e8a5161630121f9">DiffusionReactionMaterial</a>(<a class="code" href="class_s_p_h_1_1_base_reaction_model.html">BaseReactionModel</a>* species_reaction)</div>
<div class="line"><a name="l00252"></a><span class="lineno">  252</span>&#160;            : BaseMaterialType(), number_of_species_(0), species_reaction_(species_reaction) </div>
<div class="line"><a name="l00253"></a><span class="lineno">  253</span>&#160;        {</div>
<div class="line"><a name="l00254"></a><span class="lineno">  254</span>&#160;            BaseMaterialType::material_name_ = <span class="stringliteral">&quot;DiffusionReactionMaterial&quot;</span>;</div>
<div class="line"><a name="l00255"></a><span class="lineno">  255</span>&#160;        };</div>
<div class="line"><a name="l00256"></a><span class="lineno">  256</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html">DiffusionReactionMaterial</a>() {};</div>
<div class="line"><a name="l00257"></a><span class="lineno">  257</span>&#160; </div>
<div class="line"><a name="l00258"></a><span class="lineno">  258</span>&#160;        <span class="keywordtype">size_t</span> NumberOfSpecies() { <span class="keywordflow">return</span> number_of_species_; };</div>
<div class="line"><a name="l00259"></a><span class="lineno">  259</span>&#160;        <span class="keywordtype">size_t</span> NumberOfSpeciesDiffusion() { <span class="keywordflow">return</span> species_diffusion_.size(); };</div>
<div class="line"><a name="l00260"></a><span class="lineno">  260</span>&#160;        StdVec&lt;BaseDiffusion*&gt; SpeciesDiffusion() { <span class="keywordflow">return</span> species_diffusion_; };</div>
<div class="line"><a name="l00261"></a><span class="lineno">  261</span>&#160;        BaseReactionModel* SpeciesReaction() { <span class="keywordflow">return</span> species_reaction_; };</div>
<div class="line"><a name="l00262"></a><span class="lineno">  262</span>&#160;        std::map&lt;std::string, size_t&gt; SpeciesIndexMap() { <span class="keywordflow">return</span>  species_indexes_map_; };</div>
<div class="line"><a name="l00263"></a><span class="lineno">  263</span>&#160;        <span class="keywordtype">void</span> assignDiffusionReactionParticles(DiffusionReactionParticles&lt;BaseParticlesType, </div>
<div class="line"><a name="l00264"></a><span class="lineno">  264</span>&#160;            BaseMaterialType&gt;* diffusion_reaction_particles) </div>
<div class="line"><a name="l00265"></a><span class="lineno">  265</span>&#160;        {</div>
<div class="line"><a name="l00266"></a><span class="lineno">  266</span>&#160;            diffusion_reaction_particles_ = diffusion_reaction_particles;</div>
<div class="line"><a name="l00267"></a><span class="lineno">  267</span>&#160;            <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> k = 0; k &lt; species_diffusion_.size(); ++k)</div>
<div class="line"><a name="l00268"></a><span class="lineno">  268</span>&#160;                species_diffusion_[k]-&gt;assignBaseParticles(diffusion_reaction_particles);</div>
<div class="line"><a name="l00269"></a><span class="lineno">  269</span>&#160;        };</div>
<div class="line"><a name="l00274"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_material.html#a07649784c6535035ad8331c87ec19e30">  274</a></span>&#160;        Real <a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html#a07649784c6535035ad8331c87ec19e30">getDiffusionTimeStepSize</a>(Real smoothing_length) </div>
<div class="line"><a name="l00275"></a><span class="lineno">  275</span>&#160;        {</div>
<div class="line"><a name="l00276"></a><span class="lineno">  276</span>&#160;            Real diff_coff_max = 0.0;</div>
<div class="line"><a name="l00277"></a><span class="lineno">  277</span>&#160;            <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> k = 0; k &lt; species_diffusion_.size(); ++k)</div>
<div class="line"><a name="l00278"></a><span class="lineno">  278</span>&#160;                diff_coff_max = SMAX(diff_coff_max, species_diffusion_[k]-&gt;getReferenceDiffusivity());</div>
<div class="line"><a name="l00279"></a><span class="lineno">  279</span>&#160;            Real dimension = Real(Vecd(0).size());</div>
<div class="line"><a name="l00280"></a><span class="lineno">  280</span>&#160;            <span class="keywordflow">return</span> 0.5 * smoothing_length * smoothing_length / diff_coff_max / dimension;</div>
<div class="line"><a name="l00281"></a><span class="lineno">  281</span>&#160;        };</div>
<div class="line"><a name="l00283"></a><span class="lineno">  283</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> initializeDiffusion() = 0;</div>
<div class="line"><a name="l00284"></a><span class="lineno">  284</span>&#160;        <span class="keyword">virtual</span> <a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html">DiffusionReactionMaterial&lt;BaseParticlesType, BaseMaterialType&gt;</a>* </div>
<div class="line"><a name="l00285"></a><span class="lineno">  285</span>&#160;            ThisObjectPtr()<span class="keyword"> override </span>{ <span class="keywordflow">return</span> <span class="keyword">this</span>; };  </div>
<div class="line"><a name="l00286"></a><span class="lineno">  286</span>&#160;    };</div>
<div class="line"><a name="l00287"></a><span class="lineno">  287</span>&#160; </div>
<div class="line"><a name="l00292"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_mono_field_electro_physiology.html">  292</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_mono_field_electro_physiology.html">MonoFieldElectroPhysiology</a> </div>
<div class="line"><a name="l00293"></a><span class="lineno">  293</span>&#160;        : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html">DiffusionReactionMaterial</a>&lt;SolidParticles, Solid&gt;</div>
<div class="line"><a name="l00294"></a><span class="lineno">  294</span>&#160;    {</div>
<div class="line"><a name="l00295"></a><span class="lineno">  295</span>&#160;    <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00296"></a><span class="lineno">  296</span>&#160;        Real diff_cf_;</div>
<div class="line"><a name="l00297"></a><span class="lineno">  297</span>&#160;        Real bias_diff_cf_; </div>
<div class="line"><a name="l00298"></a><span class="lineno">  298</span>&#160;        Vecd bias_direction_;</div>
<div class="line"><a name="l00299"></a><span class="lineno">  299</span>&#160; </div>
<div class="line"><a name="l00300"></a><span class="lineno">  300</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> assignDerivedMaterialParameters()<span class="keyword"> override</span></div>
<div class="line"><a name="l00301"></a><span class="lineno">  301</span>&#160;<span class="keyword">        </span>{</div>
<div class="line"><a name="l00302"></a><span class="lineno">  302</span>&#160;            <a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html">DiffusionReactionMaterial&lt;SolidParticles, Solid&gt;::assignDerivedMaterialParameters</a>();</div>
<div class="line"><a name="l00303"></a><span class="lineno">  303</span>&#160;        };</div>
<div class="line"><a name="l00304"></a><span class="lineno">  304</span>&#160;    <span class="keyword">public</span>:</div>
<div class="line"><a name="l00305"></a><span class="lineno">  305</span>&#160;        <a class="code" href="class_s_p_h_1_1_mono_field_electro_physiology.html">MonoFieldElectroPhysiology</a>(<a class="code" href="class_s_p_h_1_1_electro_physiology_reaction.html">ElectroPhysiologyReaction</a>* electro_physiology_reaction);</div>
<div class="line"><a name="l00306"></a><span class="lineno">  306</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_mono_field_electro_physiology.html">MonoFieldElectroPhysiology</a>() {};</div>
<div class="line"><a name="l00307"></a><span class="lineno">  307</span>&#160; </div>
<div class="line"><a name="l00308"></a><span class="lineno">  308</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> initializeDiffusion() <span class="keyword">override</span>;</div>
<div class="line"><a name="l00309"></a><span class="lineno">  309</span>&#160;    };</div>
<div class="line"><a name="l00310"></a><span class="lineno">  310</span>&#160; </div>
<div class="line"><a name="l00315"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_local_mono_field_electro_physiology.html">  315</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_local_mono_field_electro_physiology.html">LocalMonoFieldElectroPhysiology</a> </div>
<div class="line"><a name="l00316"></a><span class="lineno">  316</span>&#160;        : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_mono_field_electro_physiology.html">MonoFieldElectroPhysiology</a></div>
<div class="line"><a name="l00317"></a><span class="lineno">  317</span>&#160;    {</div>
<div class="line"><a name="l00318"></a><span class="lineno">  318</span>&#160;    <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00319"></a><span class="lineno">  319</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> assignDerivedMaterialParameters()<span class="keyword"> override</span></div>
<div class="line"><a name="l00320"></a><span class="lineno">  320</span>&#160;<span class="keyword">        </span>{</div>
<div class="line"><a name="l00321"></a><span class="lineno">  321</span>&#160;            MonoFieldElectroPhysiology::assignDerivedMaterialParameters();</div>
<div class="line"><a name="l00322"></a><span class="lineno">  322</span>&#160;        };</div>
<div class="line"><a name="l00323"></a><span class="lineno">  323</span>&#160;    <span class="keyword">public</span>:</div>
<div class="line"><a name="l00324"></a><span class="lineno">  324</span>&#160;        <a class="code" href="class_s_p_h_1_1_local_mono_field_electro_physiology.html">LocalMonoFieldElectroPhysiology</a>(<a class="code" href="class_s_p_h_1_1_electro_physiology_reaction.html">ElectroPhysiologyReaction</a>* electro_physiology_reaction)</div>
<div class="line"><a name="l00325"></a><span class="lineno">  325</span>&#160;            :<a class="code" href="class_s_p_h_1_1_mono_field_electro_physiology.html">MonoFieldElectroPhysiology</a>(electro_physiology_reaction) {</div>
<div class="line"><a name="l00326"></a><span class="lineno">  326</span>&#160;            MonoFieldElectroPhysiology::material_name_ = <span class="stringliteral">&quot;LocalMonoFieldElectroPhysiology&quot;</span>;</div>
<div class="line"><a name="l00327"></a><span class="lineno">  327</span>&#160;        };</div>
<div class="line"><a name="l00328"></a><span class="lineno">  328</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_local_mono_field_electro_physiology.html">LocalMonoFieldElectroPhysiology</a>() {};</div>
<div class="line"><a name="l00329"></a><span class="lineno">  329</span>&#160; </div>
<div class="line"><a name="l00330"></a><span class="lineno">  330</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> initializeDiffusion() <span class="keyword">override</span>;</div>
<div class="line"><a name="l00331"></a><span class="lineno">  331</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> readFromXmlForLocalParameters(std::string&amp; filefullpath) <span class="keyword">override</span>;</div>
<div class="line"><a name="l00332"></a><span class="lineno">  332</span>&#160;    };</div>
<div class="line"><a name="l00333"></a><span class="lineno">  333</span>&#160;}</div>
</div><!-- fragment --></div><!-- contents -->
<div class="ttc" id="aclass_s_p_h_1_1_isotropic_diffusion_html"><div class="ttname"><a href="class_s_p_h_1_1_isotropic_diffusion.html">SPH::IsotropicDiffusion</a></div><div class="ttdoc">isotropic diffusion property.</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:68</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_isotropic_diffusion_html_ab1406312fbceea5607a7edd01453920f"><div class="ttname"><a href="class_s_p_h_1_1_isotropic_diffusion.html#ab1406312fbceea5607a7edd01453920f">SPH::IsotropicDiffusion::diff_cf_</a></div><div class="ttdeci">Real diff_cf_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:71</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_electro_physiology_reaction_html"><div class="ttname"><a href="class_s_p_h_1_1_electro_physiology_reaction.html">SPH::ElectroPhysiologyReaction</a></div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:173</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_base_material_html"><div class="ttname"><a href="class_s_p_h_1_1_base_material.html">SPH::BaseMaterial</a></div><div class="ttdoc">Base of all materials.</div><div class="ttdef"><b>Definition:</b> base_material.h:52</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_directional_diffusion_html"><div class="ttname"><a href="class_s_p_h_1_1_directional_diffusion.html">SPH::DirectionalDiffusion</a></div><div class="ttdoc">Diffussion is biased along a specific direction.</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:90</div></div>
<div class="ttc" id="aclass_vecd_html"><div class="ttname"><a href="class_vecd.html">Vecd</a></div></div>
<div class="ttc" id="aclass_s_p_h_1_1_electro_physiology_particles_html"><div class="ttname"><a href="class_s_p_h_1_1_electro_physiology_particles.html">SPH::ElectroPhysiologyParticles</a></div><div class="ttdoc">A group of particles with electrophysiology particle data.</div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:98</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_local_directional_diffusion_html"><div class="ttname"><a href="class_s_p_h_1_1_local_directional_diffusion.html">SPH::LocalDirectionalDiffusion</a></div><div class="ttdoc">Diffusion is biased along a specific direction.</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:126</div></div>
<div class="ttc" id="asolid__particles_8h_html"><div class="ttname"><a href="solid__particles_8h.html">solid_particles.h</a></div><div class="ttdoc">This is the derived class of base particles.</div></div>
<div class="ttc" id="abase__material_8h_html"><div class="ttname"><a href="base__material_8h.html">base_material.h</a></div><div class="ttdoc">This is the base classes of all materials. A function in a derived material class returns a value wit...</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_local_mono_field_electro_physiology_html"><div class="ttname"><a href="class_s_p_h_1_1_local_mono_field_electro_physiology.html">SPH::LocalMonoFieldElectroPhysiology</a></div><div class="ttdoc">material class for electro_physiology with locally oriented fibers.</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:315</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_base_particles_html"><div class="ttname"><a href="class_s_p_h_1_1_base_particles.html">SPH::BaseParticles</a></div><div class="ttdoc">Particles with essential (geometric and kinematic) data. There are three types of particles， all part...</div><div class="ttdef"><b>Definition:</b> base_particles.h:65</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_aliev_panfilow_model_html"><div class="ttname"><a href="class_s_p_h_1_1_aliev_panfilow_model.html">SPH::AlievPanfilowModel</a></div><div class="ttdoc">The simplest Electrophysiology Reaction model, which reduces the complex of array of ion currents to ...</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:196</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_diffusion_reaction_material_html_ac3b04fe5b64e8374b18142c63dcadc74"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_material.html#ac3b04fe5b64e8374b18142c63dcadc74">SPH::DiffusionReactionMaterial::DiffusionReactionMaterial</a></div><div class="ttdeci">DiffusionReactionMaterial()</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:245</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_diffusion_reaction_particles_html"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_particles.html">SPH::DiffusionReactionParticles</a></div><div class="ttdoc">A group of particles with diffusion or/and reactions particle data.</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:43</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_base_reaction_model_html"><div class="ttname"><a href="class_s_p_h_1_1_base_reaction_model.html">SPH::BaseReactionModel</a></div><div class="ttdoc">Base class for all reaction models.</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:154</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_diffusion_reaction_material_html"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_material.html">SPH::DiffusionReactionMaterial</a></div><div class="ttdoc">Complex material for diffusion or/and reactions.</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:222</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_diffusion_reaction_material_html_a129c308dd850749a9e8a5161630121f9"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_material.html#a129c308dd850749a9e8a5161630121f9">SPH::DiffusionReactionMaterial::DiffusionReactionMaterial</a></div><div class="ttdeci">DiffusionReactionMaterial(BaseReactionModel *species_reaction)</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:251</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_aliev_panfilow_model_html_ac926a3fcc24e3f7b65e2d87fa59662b4"><div class="ttname"><a href="class_s_p_h_1_1_aliev_panfilow_model.html#ac926a3fcc24e3f7b65e2d87fa59662b4">SPH::AlievPanfilowModel::k_</a></div><div class="ttdeci">Real k_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:200</div></div>
<div class="ttc" id="anamespace_s_p_h_html_abae56fd7f25f13487c7943ce4681d0ce"><div class="ttname"><a href="namespace_s_p_h.html#abae56fd7f25f13487c7943ce4681d0ce">SPH::IndexVector</a></div><div class="ttdeci">StdVec&lt; size_t &gt; IndexVector</div><div class="ttdef"><b>Definition:</b> sph_data_conainers.h:38</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_diffusion_reaction_material_html_a07649784c6535035ad8331c87ec19e30"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_material.html#a07649784c6535035ad8331c87ec19e30">SPH::DiffusionReactionMaterial::getDiffusionTimeStepSize</a></div><div class="ttdeci">Real getDiffusionTimeStepSize(Real smoothing_length)</div><div class="ttdoc">Get diffusion time step size. Here, I follow the reference: https://www.uni-muenster....</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:274</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_mono_field_electro_physiology_html"><div class="ttname"><a href="class_s_p_h_1_1_mono_field_electro_physiology.html">SPH::MonoFieldElectroPhysiology</a></div><div class="ttdoc">material class for electro_physiology.</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:292</div></div>
<div class="ttc" id="aclass_real_html"><div class="ttname"><a href="class_real.html">Real</a></div></div>
<div class="ttc" id="anamespace_s_p_h_html"><div class="ttname"><a href="namespace_s_p_h.html">SPH</a></div><div class="ttdef"><b>Definition:</b> solid_body_supplementary.cpp:9</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_directional_diffusion_html_abc4879e198a2fd6cf4bb19c68e8a3d4d"><div class="ttname"><a href="class_s_p_h_1_1_directional_diffusion.html#abc4879e198a2fd6cf4bb19c68e8a3d4d">SPH::DirectionalDiffusion::transformed_diffusivity_</a></div><div class="ttdeci">Matd transformed_diffusivity_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:95</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_directional_diffusion_html_a2d7e6efe0bd23b2f8a483563270298c5"><div class="ttname"><a href="class_s_p_h_1_1_directional_diffusion.html#a2d7e6efe0bd23b2f8a483563270298c5">SPH::DirectionalDiffusion::bias_diff_cf_</a></div><div class="ttdeci">Real bias_diff_cf_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:94</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_base_diffusion_html"><div class="ttname"><a href="class_s_p_h_1_1_base_diffusion.html">SPH::BaseDiffusion</a></div><div class="ttdoc">diffusion property abstract base class.</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:49</div></div>
<div class="ttc" id="anamespace_s_p_h_html_a341a68e44d4d73463e7fcfe4f09e521e"><div class="ttname"><a href="namespace_s_p_h.html#a341a68e44d4d73463e7fcfe4f09e521e">SPH::ReactionFunctor</a></div><div class="ttdeci">std::function&lt; Real(StdVec&lt; StdLargeVec&lt; Real &gt;&gt; &amp;, size_t particle_i)&gt; ReactionFunctor</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:149</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_directional_diffusion_html_a6c1e25784f768cb1caffb38ab17332e4"><div class="ttname"><a href="class_s_p_h_1_1_directional_diffusion.html#a6c1e25784f768cb1caffb38ab17332e4">SPH::DirectionalDiffusion::bias_direction_</a></div><div class="ttdeci">Vecd bias_direction_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:93</div></div>
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